• Capturing workflows and improving methods reproducibility (Goodman, Fanelli, and Ioannidis 2016)

<"https://www.google.com/search?q=workflow">

• Idea/question/hypotheses
• Design study
• Seek ethics board permission
• Build/borrow/buy data collection instruments
• Run study
• Analyze results
• Write-up results for presentation and/or publication

• Participants
  • Number, characteristics
• Setting(s)
  • Lab, classroom, home
• Measures or tasks
  • Self/other report
  • Observations/video or audio recording
  • Physiological measures (MRI, EEG, ECG)
  • Computer-based tasks

• Surveys
• Video/audio
• MRI, EEG, ECG
• Computer-generated data files

done.collecting.data = FALSE
while (!done.collecting.data) {
  Collect.sample()
  if (collected.sample.n >= planned.sample.n) {
    done.collecting.data = TRUE
  } else {
    done.collecting.data = FALSE
  }
}

• Clean/check data
• Merge, combine, munge data

• Intro
• Methods
• Results
  • Stats
  • Plots
• Conclusions
• References
• Data?

• Idea/question/hypotheses
• Design study
• Seek ethics board permission
• Build/borrow/buy data collection instruments
• Run study
• Analyze results
• Write-up results for presentation and/or publication

• Data collection instruments
• Running study
• Data analysis
• Study write-up

• Maximize consistency, methods reproducibility (Goodman, Fanelli, and Ioannidis 2016)
• Design of/consistent adherence to detailed experimental protocols
• Consistent, transparent workflows
• Consistent, transparent organization of data, metadata
• Minimize human/hand data entry
• Automate as much as possible

• Play & Learning Across a Year (PLAY) project wiki

• What data and metadata am I collecting?
• How does it get collected?
• Where does it go after it's collected?
• How does my non-electronic data get transferred to an electronic form?
• How do my electronic data files get cleaned, merged, munged?

• "Chain of custody" from raw data to finished results and figures
• Single command to regenerate all results and figures from raw data

http://datasci.kitzes.com/lessons/python/reproducible_workflow.html

• Create consistent structure for projects
  • Use file name conventions
• Use machine-readable file types
  • commas-separated value (.csv) vs. .xlsx
• Automate as much as possible
• Use version control

study-1/
  sub-001/
    sub-001-measure-a.txt
    sub-001-image.jpg
    sub-001-demo.csv
    sub-001-measure-b.txt
  sub-002/
    sub-002-measure-a.txt
    sub-002-image.jpg
    sub-002-demo.csv
    sub-002-measure-b.txt
  ...
  sub-00n/
    ...

study-1/
  measure-a/
    sub-001-measure-a.txt
    ...
  measure-b/
    sub-001-measure-b.txt
    ...
  image/
    sub-001-image.jpg
    sub-002-image.jpg
    ...
  demo/
    sub-001-demo.csv
    sub-002-demo.csv
    ...

study-1/
  analysis/
    data/
      sessions/
        2017-01-09-sub-001/
        ...
      aggregate/
        study-1-demo-aggregate.csv
        study-1-measure-a-aggregate.csv
        ...
    R/
    img/
    reports/
  protocol/
    code/
      my-experiment.m
    materials/
      stim-1.jpg
      stim-2.jpg
      ...

  pubs/
    presentations/
    papers/
  refs/
  grants/
    2016/
    2017/
  irb/
  mtgs/

https://nyu.databrary.org/volume/2

• Automates some of the project management involved in data analysis
  • Hat Tip (HT): Michael Hallquist
• Gilmore says: Use what you like

## Create project directory
proj.name = "tmp_proj"
if (!exists(proj.name)) {
  dir.create(path = proj.name, recursive = TRUE)
}

# Create sessions directory
sessions.dir = paste(proj.name, "analysis/sessions", sep="/")
if (!exists(sessions.dir)) {
  dir.create(path = sessions.dir, recursive = TRUE) # creates intermediate dirs
}

# Aggregate data file directory
agg.dir = paste(proj.name, "analysis/aggregate", sep="/")
if (!exists(agg.dir)) {
  dir.create(path = agg.dir, recursive = TRUE)
}

• Use consistent file/directory names
  • lowerCamelCaseIsGood.txt so is UpperCamelCase.txt
  • underscores_between_words.txt works; so do dashes-between.txt
  • avoid spaces in your file names.txt; these are not always reliably readable by all computers.
• Choose good, descriptive names

• Be consistent
• Write dates as YYYY-MM-DD.
• Fill-in all cells
• One thing in a cell
• Make your data a rectangle
• Create a data dictionary

• No calculations in raw data files
• No font or color to highlight data
• Make back-ups
• Validate data to avoid data entry errors
• Save data in plain text files (comma or tab-delimited)

• Data scientists (that's you!) spend a lot of time just cleaning data
• http://www.infoworld.com/article/3047584/big-data/hottest-job-data-scientists-say-theyre-still-mostly-digital-janitors.html

• study-1-demo-agg.csv contains
  • subID, sex, ageYrs, favColor
• study-1-rt-agg.csv contains
  • subID, condition, rt

subID,sex,ageYrs,favColor
001,m,53,green
002,f,51,blue
003,f,23,red
004,m,25,aqua

Don't put spaces between variables in comma-separated value (.csv) files. Also, make sure to add a final line feed/enter character.

subID,condition,rt
001,upright,250
001,inverted,300
002,upright,225
002,inverted,290
003,upright,270
003,inverted,230
004,upright,210
004,inverted,240

# read data files, first row (header) contains variable names
demo <- read.csv(file = "csv/study-1-demo-agg.csv", header = TRUE)
rt <- read.csv(file = "csv/study-1-rt-agg.csv", header = TRUE)

# merge and print
merged <- merge(demo, rt, by = "subID")
merged

##   subID sex ageYrs favColor condition  rt
## 1     1   m     53    green   upright 250
## 2     1   m     53    green  inverted 300
## 3     2   f     51     blue   upright 225
## 4     2   f     51     blue  inverted 290
## 5     3   f     23      red   upright 270
## 6     3   f     23      red  inverted 230
## 7     4   m     25     aqua   upright 210
## 8     4   m     25     aqua  inverted 240

• Variables in columns
• Observations in rows
• Ok/better to repeat values in columns
  • subID,trial,rt
  • 001,1,300
  • 001,2,345
  • 002,2,327
  • 003,3,429

• Think like a computer!
• Plan your work; work your plan
• Consistency, standard formats
• Tidy data
• Haven't said anything about "openness"…yet

• Data Carpentry, http://www.datacarpentry.org/
• Software Carpentry, https://software-carpentry.org/
• Open Science Framework (OSF), http://osf.io
• R for Data Science, http://r4ds.had.co.nz/

• Edit/create a text-based workflow for an active project you are working on.
  • Annote the workflow to indicate where it could be made more reproducible, transparent.